Ni Gui-Yan, Zhang Zhe, Jiang Li, Ma Pei-Pei, Zhang Qin, Ding Xing-Dong
College of Animal Science and Technology, China Agricultural University, Beijing, China.
Yi Chuan. 2012 Jan;34(1):50-8. doi: 10.3724/sp.j.1005.2012.00050.
Effective populations size (Ne) is an important population parameter that helps to explain genetic variation, population evolution and understanding of the genetic architecture underlying complex traits. With the availability of high-dense SNP panels, more and more researches focus on estimating of Ne using linkage disequilibrium (LD) between SNPs. In this study, we estimated the effective population size from 2093 Chinese Holstein Cattle genotyped with Illumina BovineSNP50 BeadChip. After removal of individual with call rate lt; 95%, SNPs with call rate lt; 95%, minor allele frequency lt; 5% and Hardy-Weinberg Equilibrium test with Plt;0.0001, 1 968 individuals with 38 796 SNPs were remained. Eight kinds of SNP pairs with the distances 0.1, 0.2, 0.5, 1, 2, 5, 10, and 15 Mb were respectively chosen to estimate the effective population size of Chinese Holstein cattle from 4 generations ago. It is demonstrated from the results of this study that the effective population size of Chinese Holstein is decreased in the past generations, and the corresponding effective population size at ~4 generations ago is only around 45.
有效种群大小（Ne）是一个重要的种群参数，有助于解释遗传变异、种群进化以及理解复杂性状背后的遗传结构。随着高密度SNP芯片的出现，越来越多的研究聚焦于利用SNP之间的连锁不平衡（LD）来估计Ne。在本研究中，我们对2093头中国荷斯坦奶牛进行了基因分型，使用的是Illumina BovineSNP50 BeadChip芯片。在去除检出率<95%的个体、检出率<95%的SNP、次要等位基因频率<5%以及经P<0.0001的哈迪-温伯格平衡检验后，剩余1968个个体和38796个SNP。分别选择了距离为0.1、0.2、0.5、1、2、5、10和15 Mb的8种SNP对来估计4代以前中国荷斯坦奶牛的有效种群大小。本研究结果表明，中国荷斯坦奶牛的有效种群大小在过去几代中有所下降，约4代以前相应的有效种群大小仅约为45。
